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Advice for WaterFurnace problems

We built a new home and installed a WaterFurnace geothermal system in November 2011. The system is set up with 4 zones, 3 on the main floor and one for the basement. We live on a lake in NC and the coils are 13' deep in the lake. From the time it was installed, it worked perfectly. We were able to adjust all thermostats to control individual temperatures, and keep the settings lower in the winter and warmer in the summer. Bills were low and the house (which has complete envelope foam insulation) was quite comfortable. We also installed hot water from this system to the HW heater.

Then last fall we got a "Call for Service" notification on all of the thermostats. Our technician (very motivated and helpful) came out and found a problem where the pipe leading to the HW heater had steam coming from it. He shut that down. After consulting with WaterFurnace, and doing some additional testing, they determined that the problem was the main board, the thermistor, and the shutoff valve. After a while they replaced these.

But while waiting for this repair, and even after replacement, we keep getting "Call for Service". So we did some testing. First we tested all thermostats to see if leaving one off would keep the system from needing service. It turned out that the one on the west side of the house was the culprit. As long as we left this off, we never got a "Call for Service." So we swapped two of the thermostats and the west zone still had the problem, meaning that it wasn't the thermostat, it was the zone. In the meantime, our home is no longer comfortable, and the bills have increased by 50% over what they had been last year. Since recent weather has been more temperate, I can't attribute this to temperature.

Today, our technician brought an expert from WaterFurnace with him. This person has 15 years of experience with Geothermal systems. At the end of the discussion, they told my wife that (1) the problem is that when a single zone is running, there is too little airflow though the constricted ducts, and the system overheats, and (2) the reason that the bills have gone up is that when the system overheats, it uses the emergency electric heat. So, as a temporary measure until they have a better idea what to do, they have increased the airflow from 25% to 70% in the west zone (or may be in all zones - I wasn't there and my wife didn't tell me).

So my question is this. If a WaterFurnace system is set up to be zoned in four zones, why is ours having this problem? And does their explanation of what is happening with the system overheating and the emergency electric heat kicking in make sense?